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- PDB-1tm4: crystal structure of the complex of subtilsin BPN'with chymotryps... -

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Basic information

Entry
Database: PDB / ID: 1tm4
Titlecrystal structure of the complex of subtilsin BPN'with chymotrypsin inhibitor 2 M59G mutant
Components
  • Subtilisin BPN' precursor
  • chymotrypsin inhibitor 2
KeywordsHYDROLASE / serine protease / inhibitor
Function / homology
Function and homology information


subtilisin / sporulation resulting in formation of a cellular spore / fibrinolysis / serine-type endopeptidase inhibitor activity / response to wounding / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / : / Fervidolysin N-terminal prodomain / Trypsin Inhibitor V; Chain A / Subtilisin Carlsberg-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily ...Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / : / Fervidolysin N-terminal prodomain / Trypsin Inhibitor V; Chain A / Subtilisin Carlsberg-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / : / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Subtilisin BPN' / Chymotrypsin inhibitor 2
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
Hordeum vulgare subsp. vulgare (domesticated barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRadisky, E.S. / Kwan, G. / Karen Lu, C.J. / Koshland Jr., D.E.
CitationJournal: Biochemistry / Year: 2004
Title: Binding, Proteolytic, and Crystallographic Analyses of Mutations at the Protease-Inhibitor Interface of the Subtilisin BPN'/Chymotrypsin Inhibitor 2 Complex(,).
Authors: Radisky, E.S. / Kwan, G. / Karen Lu, C.J. / Koshland Jr., D.E.
History
DepositionJun 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.5Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Subtilisin BPN' precursor
I: chymotrypsin inhibitor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7539
Polymers35,5912
Non-polymers1,1627
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-24 kcal/mol
Surface area13360 Å2
MethodPISA
2
E: Subtilisin BPN' precursor
I: chymotrypsin inhibitor 2
hetero molecules

E: Subtilisin BPN' precursor
I: chymotrypsin inhibitor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,50618
Polymers71,1824
Non-polymers2,32414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+1/31
Buried area7180 Å2
ΔGint-54 kcal/mol
Surface area25740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.100, 94.100, 186.806
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 2 types, 2 molecules EI

#1: Protein Subtilisin BPN' precursor / Subtilisin Novo / Alkaline protease


Mass: 28381.396 Da / Num. of mol.: 1 / Mutation: C-terminal 6-His tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: APR / Plasmid: pSER25 / Production host: Bacillus subtilis (bacteria) / Strain (production host): BG2036 / References: UniProt: P00782, subtilisin
#2: Protein chymotrypsin inhibitor 2


Mass: 7209.457 Da / Num. of mol.: 1 / Mutation: I45A,I59G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare subsp. vulgare (domesticated barley)
Species: Hordeum vulgare / Strain: subsp. vulgare / Plasmid: pCI2M59G / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q40059

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Non-polymers , 5 types, 446 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: sodium citrate, isopropanol, PEG 400, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 10, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→81.65 Å / Num. all: 54020 / Num. obs: 54020 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 17.6 % / Rsym value: 0.112 / Net I/σ(I): 19.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALAdata scaling
TRUNCATEdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1tm3

1tm3


Resolution: 1.7→81.65 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.556 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / ESU R: 0.076 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18313 2697 5 %inherited from 1tm3
Rwork0.15786 ---
all0.15914 54020 --
obs0.15914 51323 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.17 Å20 Å2
2--0.35 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.7→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 67 439 3054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212660
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9553608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7395345
X-RAY DIFFRACTIONr_chiral_restr0.1330.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021993
X-RAY DIFFRACTIONr_nbd_refined0.2120.21274
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2298
X-RAY DIFFRACTIONr_metal_ion_refined0.0570.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4220.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.235
X-RAY DIFFRACTIONr_mcbond_it0.8871.51714
X-RAY DIFFRACTIONr_mcangle_it1.51122763
X-RAY DIFFRACTIONr_scbond_it2.6963946
X-RAY DIFFRACTIONr_scangle_it4.5644.5844
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.265 176
Rwork0.253 3516

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